The Knight's code of conduct

I was in the Gnomish mines getting to level 5 to dip for Excalibur when a Gnome fled and I let him be due to my code of conduct. Went down another level and destroyed some more gnomes before coming back up. "Another" Gnome tried to attack me and when I killed him it called me a caitiff. That was the Gnome that fled from me...

How am I supposed to know that so I can avoid it in the future? I wouldn't have attacked him if I knew!

If you have a stethoscope or wand of probing you can use it on the monster. If it tells you that the monster is scared, attacking it would violate your code of conduct.

Without these items there's no way to know for sure other than observing the monster for a couple of turns and see whether it looks like it's fleeing (note that the monster attacking you does not necessarily mean it is not scared, which is kind of unfair, but such is life).

That being said the penalties for these violations aren't too severe, so unless you attack fleeing monsters a lot, you don't need to worry about it.